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The San Francisco Bay and Delta - An Estuary Undergoing Change
Frederic H. Nichols


The San Francisco Bay estuary, at the confluence of the Sacramento and San Joaquin Rivers in central California, is renowned for its natural beauty, international commerce, recreation, and sports fishing. However, the estuary has been greatly modified by 150 years of intensifying human activity (Nichols et al. 1986).

More than 95% of the historic tidal marshes have been leveed and filled (Fig. 1), with attendant losses in fish and wildlife habitat. The flow of freshwater into the estuary has been greatly reduced by water diversions largely to support irrigated agriculture. Harbor and channel dredging has changed both the dredged and disposal sites and altered water flow patterns and salinity. Contaminants enter the estuary in municipal and industrial sewage, and urban and agricultural runoff. Introduced exotic species continue to change the Bay's biota by altering its food webs. All of these changes have had marked effects on the estuary's biological resources, particularly well documented by declines in abundance of fish species (San Francisco Estuary Project Management Committee 1994).

The San Francisco Bay estuary and Delta at the time of the discovery of gold in the Sierra Nevada foothillsThe San Francisco Bay estuary and Delta at present

Figure 1. The San Francisco Bay estuary and Delta at the time of the discovery of gold in the Sierra Nevada foothills (first panel) and at present (second panel).

It is not clear which and to what extent particular human activities are responsible for specific unwanted ecosystem changes. Thus, determining which courses of action would be most effective in bringing about improvements in the estuary's water quality and restoration of its fish populations has been difficult. At the same time, there is concern about: potential limitations to additional economic development because of demands on land and water supplies; increasing constraints on diverting water away from the Delta because of concerns for endangered species; pressures to shift consumption of managed water from agricultural use to urban use; future land subsidence as a result of increasing dependence on ground water supplies in dry years; further loss of tidal wetlands to urban encroachment; and constraints on harbor improvements because of potential changes in salinity and contaminant levels as a result of dredging and spoils disposal.

Recognition of the conflicts among the many uses of the Bay/Delta system have brought the public, resource managers and regulators, and elected officials to recognize the great need for credible, unbiased scientific information on the significance of river flow diversion, contaminant inputs, dredging, and habitat alteration (San Francisco Estuary Project Management Committee 1994).

The USGS, with internationally recognized interdisciplinary expertise and experience in the study of estuarine processes and as a long-time leader in studies of the San Francisco Bay estuary, has provided much of the fundamental knowledge of and interrelations among the hydrology, geology, chemistry and ecology of this complex estuarine system. For example, USGS studies have documented changes in the estuary's shoreline; changes in patterns of water and sediment movement; the contamination of its water, sediments and organisms; and alterations of its biological communities. The USGS is now focusing field, laboratory and modeling studies on: (1) the effects of freshwater flow on the estuary's chemistry and biology; (2) the distribution and influence of contaminants on estuarine invertebrates; (3) and the processes influencing the character and stability of remaining wetlands.

Effects of Freshwater Flow

Changes in the quantity, timing, and quality of fresh water flowing into the Delta and Bay, as a result of diversion via pumps within the Delta (Fig. 1), is implicated in declines of fish species both because of physical removal of young fish by the pumps as well as habitat changes resulting from changing flow patterns and salinity distributions. The US Environmental Protection Agency has proposed a salinity standard that would require the salt content of the water in ecologically sensitive regions of the estuary to be maintained at specified levels. There is need for a better quantitative understanding of flow patterns and salinity distributions within the Delta and Suisun Bay and the relations between the two.

The USGS has conducted broad-scale field and modeling studies that have provided detailed understanding of water movement and salinity distributions within the estuary. In cooperation with other agencies in the Interagency Ecological Program (IEP: US Fish & Wildlife Service, US Bureau of Reclamation, USGS, US Army Corps of Engineers, US Environmental Protection Agency, CA Water Resources Control Board, CA Department of Water Resources, and CA Department of Fish & Game), the USGS is applying new technologies to measure within-Delta water transfers and Delta outflow into the Bay, providing information needed for documenting salt transport mechanisms and managing freshwater flow to meet salinity standards. The USGS is also developing statistical models relating anomalous precipitation, snowpack, temperature, and atmospheric circulation to combined Sacramento/San Joaquin monthly flows.

There is increasing recognition of the important relationship between freshwater flow and contaminant transport to and through the estuary. For example, USGS studies have detected pulses of pesticides (applied during winter in the Sacramento and San Joaquin Valleys) flowing through the Delta and upper estuary during winter runoff events. These pesticides pulses have demonstrated toxicity to aquatic life in the Delta and Suisun Bay. At the same time, sediments and sediment-bound contaminants are being transported through the Delta into the Bay. Better understanding the mechanisms of dissolved contaminant and sediment transport in the Bay is necessary for estimating organism exposure and for evaluating mitigation alternatives.

Correlations between flows and most biological populations in the Bay and Delta are well documented (Jassby et al. in press). As examples, we know that river flow is a source of organic matter to support biological productivity within the estuary and that transfers of organic matter between different levels of the food web are influenced by fluctuations in freshwater inflow. We also know that flow conditions are implicated in ecological disruptions (major changes in the estuary's food web) following invasions by exotic species. Unfortunately, many of the underlying causes have not been identified. In particular, establishment of connections between flow-related habitat features and the sustainability of individual fish populations is a problem of high priority. To this end, the USGS maintains a baseline measurement program (mapping temperature, salinity, turbidity, and chlorophyll in the channel, and emphasizing sampling of benthic invertebrate species abundances and phytoplankton blooms) in San Pablo Bay, Central Bay, and the South Bay, complementing the program of the Interagency Ecological Program in the upper estuary and Delta. Additionally, USGS laboratory experimentation and modeling efforts are providing understanding of the couplings between water and sediment movement, biogeochemical cycling of nutrients, phytoplankton population dynamics and primary production, and the establishment of introduced species.

Distribution and Effects of Contaminants

Contaminants from numerous sources (Fig. 1) are pervasive throughout the estuary and its watershed. Agencies charged with protecting and enhancing the estuary's biological resources recognize the need for a much better understanding of contaminant distribution and ecological effects in order to resolve controversies with regard to the regulation of pollutant discharge.

The USGS is examining trace metal and pesticide concentrations in sediments and benthic invertebrates to provide this understanding. As examples, biological effects of pesticides entering the Bay during high river flows are being examined using local species of invertebrates in laboratory toxicity tests with exposure times similar to those experienced by animals in nature. The USGS is also using models and field studies to investigate recycling of metals and nutrients from internal sedimentary sources in the estuary.

In cooperation with the San Francisco Regional Water Quality Control Board and the US Army Corps of Engineers, the USGS is also quantifying the physical factors (e.g., tidal currents and wind waves) that control resuspension and transport of fine sediment in the shallows of the bay to assess the importance of resuspension events on metals concentrations in the water.

Wetlands Processes

The loss of 95% of the estuary's wetlands since 1850 (Fig. 1) has placed increased importance on the remaining 125 km2 of wetlands that continue to be threatened by development, erosion, pollution, and rising sea level. Wetland management agencies (e.g., the US Army Corps of Engineers and the San Francisco Bay Conservation and Development Commission) must also develop viable strategies for creating new wetlands in leveed areas used as farmland or as salt evaporating ponds that have subsided since being isolated from Bay waters. As an example, the use of dredge spoils to fill these areas raises questions about release of contaminants and changes in wetland habitat values. The USGS is participating in the restoration of a 350-acre tract of land on San Pablo Bay by monitoring the development of tidal channels and flow patterns, changes in geotechnical and geochemical properties of the pre-existing and new sediment (dredge spoils), and sedimentation patterns within the restored wetlands and adjacent areas. The USGS is also mapping wetlands distributions using remotely sensed image data and monitoring physical processes, including currents, wind, and waves, that alter wetlands and adjacent shallows, quantifying the distribution and elevations of the shoreline, and developing models that characterize the physical forces acting upon wetlands.

Information Transfer

The USGS is developing new tools and procedures to make existing and newly developed information about the San Francisco Bay Estuary and Delta conveniently available. As an example, the USGS will increase accessibility to existing spatial data scattered among several USGS laboratories by creating a World Wide Web information interface. World Wide Web navigators, such as Mosaic, will enable any user with Internet access to browse and retrieve information relevant to the San Francisco Bay/Delta, including text, pictures, maps, and animations, and interact directly with USGS experts.

The USGS long-term monitoring and research programs in San Francisco Bay provide needed data, information, interpretations, and assessments that contribute to the work of other Federal and State agencies. This linkage of science and decision making ensures the coordination of activities necessary for effective environmental resource management.


Jassby, A. D., Kimmerer, W. J., Monismith, S. G., Armor, C., Cloern, J. E., Powell, T. M., Schubel, J. R., and Vendlinski, T. J., 1995,Isohaline position as a habitat indicator for estuarine populations: Ecological Applications, v. 5.

Nichols, F. H., Cloern, J. E., Luoma, S. N., and Peterson, D. H., 1986, The modification of an estuary: Science, v. 231, p. 567-573.

San Francisco Estuary Project Management Committee, 1994, Comprehensive Conservation and Management Plan: San Francisco Estuary Project, 235 p.

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Page Last Modified: Thursday, 13-Dec-2007 12:22:15 PST